EMBOSS explorer

phiblast

Search protein sequence set combining matching of pattern with local alignment of a query sequence surrounding the match (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Query sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Pattern file:
Select search set type
Standard protein search set

User defined search set. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
User provided BLAST format databank (you can make one using makeblastdb):
Required section
Word size
E() value cutoff for display
Additional section
Maximum number of rounds
E() value threshold for inclusion in model
Amino acid comparison matrix, gap penalty, gap length penalty
Advanced section
Double hit algorithm?
Multiple hits window size
Effective databank size for statistical calculations
Output section
Keep only n best hits from same region
Show only the n best scoring sequences that satisfy E() cutoff
Show only alignments for the n first sequences (default is 250)
Alignment format
Show output of all rounds?
Make output file with profile in human readable format?
Make output file with profile in BLAST-readable format for restarting search?
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.